Hi Elaine, yes it should work for most people with a recent version of HOLE - I am using a potassium channel here as an example but I am using it for other things myself of course. Actually I just updated the script, as the channel axis pdb (sphpdb.pdb) was causing problems with molmap in some cases (new version attached).

The only thing that might need tweaking is the path to the vdw radius file (which I have pointing to a custom radius file here (nussinov.rad), but it works fine with the ‘simple.rad’ file distributed with HOLE). Otherwise it should work without modification assuming you have sed, grep, gnuplot, awk and hole. Run the script without arguments for usage instructions.

Once you have sphpdb and dotsurface. pdb, you can load both into chimera (I would suggest repr wire; bonddisplay off for the dotted surface, but YMMV - with bonddisplay on it is also a kind of nice pseudo-mesh), and then color as described in the previous email - using molmap #sphpdb_id 0.5, then ac sd with the dotted surface atoms selected to assign the attribute corresponding to radius. Let me know if you find it useful or run into any bugs.

Cheers, Oliver.

On Aug 7, 2015, at 4:06 PM, Elaine Meng meng@cgl.ucsf.edu wrote:

Hi Oliver, Very nice image! Thanks for the script; should it work for most people with a recent version of HOLE, or does it need to be tailored for a specific situation? I might keep it for myself to try later.

Sorry, I think it's a bug where “ac sd" should mark the distance attribute as something to be saved in a session, but it doesn’t.

Sorry about that… in the meanwhile, the somewhat annoying workaround (but only needs to be done once) is to save the attribute to a file, read it back in with defattr, and then save the session. The Render by Attribute dialog has menu item File… Save Attributes and that creates the correct format for reading back in with defattr.

Best, Elaine

---

Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 7, 2015, at 12:43 PM, Oliver Clarke olibclarke@gmail.com wrote:

...

Hi all,

I use the command “ac sd” to color dotted surfaces such as the attached by pore radius (I generate a molmap surface corresponding to the channel axis and then use "ac sd" to generate an attribute “distance", which in this case corresponds to the pore radius, which I can then use to color the dotted surface pdb using Render by Attribute).

The dotted surface is generated using the program HOLE (http://www.smartsci.uk/hole/) along with the attached script to make it readable by chimera.

This all works fine, however I have noted that the attribute generated by "ac sd” is not present when I reload the saved session, whereas other attributes (e.g. those created explicitly with defattr) are.

I can just regenerate it of course, but it would be convenient if it were saved with the session, as it can take a while (~10 minutes) to calculate for large dotted surfaces.

Cheers, Oliver.

<hole_chimera_script>

Thanks Tom!

As well as the dotted surface, HOLE generates a pdb consisting of atoms finely spaced along the channel axis (which is usually, but not necessarily, a straight line). I use molmap #channel_axis.pdb 0.5 or similar to generate the axis surface, which I then contour at quite a high threshold prior to running ac sd.

I did try running molmap on the dotsurface and coloring by radius - it works fine, but I really like the aesthetics of the dotted surface, and I couldn't figure out how to color the pdb the same as the molmap (which would sort of be the reverse of scolor zone I guess). There is no way to generate the same sort of radial coloring scheme for pdbs, right? It has to be done by generating an attribute and coloring accordingly?

Cheers, Oliver.

On Mon, Aug 10, 2015 at 2:52 PM, Tom Goddard goddard@sonic.net wrote:

Hi Oliver,

Cool image. Not sure how you made the axis line surface with molmap for measuring the distances — it might be easier to use “shape cylinder” to make the axis line. Another approach might be to use molmap on the PDB dot surface and then color by cylinder radius with the Surface Color dialog or scolor command.

I fixed shortcut “sd” that computes distances from atoms to a surface so that the values get saved in session files.

    Tom

...

On Aug 7, 2015, at 12:43 PM, Oliver Clarke wrote:

Hi all,

I use the command “ac sd” to color dotted surfaces such as the attached

by pore radius (I generate a molmap surface corresponding to the channel axis and then use "ac sd" to generate an attribute “distance", which in this case corresponds to the pore radius, which I can then use to color the dotted surface pdb using Render by Attribute).

...

The dotted surface is generated using the program HOLE (

http://www.smartsci.uk/hole/) along with the attached script to make it readable by chimera.

...

This all works fine, however I have noted that the attribute generated

by "ac sd” is not present when I reload the saved session, whereas other attributes (e.g. those created explicitly with defattr) are.

...

I can just regenerate it of course, but it would be convenient if it

were saved with the session, as it can take a while (~10 minutes) to calculate for large dotted surfaces.

...

Cheers, Oliver.

<dot_surf.png> <hole_chimera_script>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Oops, meant to say “there is *no* equivalent” to scolor for atoms.

Tom

On Aug 10, 2015, at 12:16 PM, Tom Goddard goddard@sonic.net wrote:

Yes there is equivalent of the surface color command scolor that colors on atoms, although it would be natural extension of scolor since that command just assigns colors at points in space.

Tom

...

On Aug 10, 2015, at 12:10 PM, Oliver Clarke wrote:

Thanks Tom!

As well as the dotted surface, HOLE generates a pdb consisting of atoms finely spaced along the channel axis (which is usually, but not necessarily, a straight line). I use molmap #channel_axis.pdb 0.5 or similar to generate the axis surface, which I then contour at quite a high threshold prior to running ac sd.

I did try running molmap on the dotsurface and coloring by radius - it works fine, but I really like the aesthetics of the dotted surface, and I couldn't figure out how to color the pdb the same as the molmap (which would sort of be the reverse of scolor zone I guess). There is no way to generate the same sort of radial coloring scheme for pdbs, right? It has to be done by generating an attribute and coloring accordingly?

Cheers, Oliver.

On Mon, Aug 10, 2015 at 2:52 PM, Tom Goddard wrote: Hi Oliver,

Cool image. Not sure how you made the axis line surface with molmap for measuring the distances — it might be easier to use “shape cylinder” to make the axis line. Another approach might be to use molmap on the PDB dot surface and then color by cylinder radius with the Surface Color dialog or scolor command.

I fixed shortcut “sd” that computes distances from atoms to a surface so that the values get saved in session files.

    Tom

...

On Aug 7, 2015, at 12:43 PM, Oliver Clarke wrote:

Hi all,

I use the command “ac sd” to color dotted surfaces such as the attached by pore radius (I generate a molmap surface corresponding to the channel axis and then use "ac sd" to generate an attribute “distance", which in this case corresponds to the pore radius, which I can then use to color the dotted surface pdb using Render by Attribute).

The dotted surface is generated using the program HOLE (http://www.smartsci.uk/hole/ http://www.smartsci.uk/hole/) along with the attached script to make it readable by chimera.

This all works fine, however I have noted that the attribute generated by "ac sd” is not present when I reload the saved session, whereas other attributes (e.g. those created explicitly with defattr) are.

I can just regenerate it of course, but it would be convenient if it were saved with the session, as it can take a while (~10 minutes) to calculate for large dotted surfaces.

Cheers, Oliver.

<dot_surf.png> <hole_chimera_script>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu mailto:Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users